| run: | |
| name: discovery_benchmark | |
| output_dir: results/discovery_benchmark | |
| random_seed: 20260415 | |
| batch_size: 32 | |
| adaptive_budget: 50000 | |
| baseline_budget: 50000 | |
| max_batches: 2000 | |
| allow_resume: true | |
| enable_adaptive_early_stop: true | |
| target: | |
| protein_name: MDM2 | |
| target_id: mdm2_discovery | |
| docking_reference_pdb: "4HG7" | |
| docking_target_path: data/targets/discovery_benchmark/mdm2_4hg7.pdb | |
| reference: | |
| reference_id: ref_nutlin3a | |
| pdb_id: "4HG7" | |
| ligand_comp_id: "NUT" | |
| benchmark_dataset: | |
| output_dir: data/ligands/discovery_benchmark | |
| target_size: 50000 | |
| shuffle_seed: 424242 | |
| reuse_existing: true | |
| min_similarity_keep: 0.08 | |
| pubchem_max_records: 120000 | |
| pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35, 32, 30] | |
| chembl_target_id: CHEMBL5023 | |
| chembl_max_rows: 120000 | |
| allow_generated_fallback: true | |
| backend: | |
| type: rdock | |
| require_real_backend: true | |
| n_runs: 5 | |
| mapper_radius: 6.0 | |
| command_timeout_seconds: 300 | |
| parallel_jobs: auto-minus-4 | |
| encoding: | |
| fingerprint_radius: 2 | |
| fingerprint_bits: 1024 | |
| generate_3d: false | |
| feature_extraction: | |
| compute_partial_charges: false | |
| compute_sasa: false | |
| clustering: | |
| butina_cutoff: 0.35 | |
| n_hyperclusters: 50 | |
| scheduler: | |
| init_coverage_fraction: 0.35 | |
| conservative_deprioritize: true | |
| surrogate: | |
| prefer_xgboost: true | |
| n_estimators: 250 | |
| min_train_samples: 20 | |
| max_depth_small: 3 | |
| max_depth_large: 6 | |
| model_weight_schedule: | |
| sample_knots: [20, 50, 100, 200, 500] | |
| weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] | |
| max_weight: 0.9 | |
| min_weight: 0.05 | |
| instability_threshold: 2.0 | |
| instability_decay: 0.25 | |
| matrix: | |
| naive_random_seeds: [11, 22, 33, 44, 55] | |
| cluster_naive_seeds: [101, 202, 303, 404, 505] | |
| include_adaptive_top1_variant: true | |
| include_adaptive: true | |
| include_naive_random: true | |
| include_cluster_naive: true | |
| modes: [docking_only, full_feature] | |
| analysis: | |
| analog_similarity_threshold: 0.65 | |
| rolling_window: 200 | |
| replicate_subset_size_top: 20 | |
| replicate_subset_size_borderline: 20 | |
| replicate_subset_size_clusters: 20 | |
| replicate_runs: 2 | |
| early_stop: | |
| min_evaluated: 3000 | |
| patience_rounds: 12 | |
| min_model_weight: 0.4 | |
| quantile: 0.15 | |
| uncertainty_weight: 0.2 | |
| min_improvement: 0.015 | |
| exploration_margin: 0.45 | |
| exploitation_margin: 0.1 | |
| reference_evaluations: 50000 | |